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Li, G.

Publications and source records attributed to Li, G..

At least 163 records · Page 9Linked to original sources

Themis dominates T cell exhaustion by regulation of TCR and PD-1 signaling

T cell exhaustion is important to protect the host from immunopathology during chronic viral infection, but it also impairs T cell anti-tumor immunity1-5. A fundamental unresolved question is whether and how T cell exhaustion is determined at the onset of TCR signaling6-8. Here we report an unexpected role of Themis, a TCR-proximal signaling molecule9, in T cell exhaustion. Chronic viral infection in mice usually leads to T cell exhaustion and survival of the host. Surprisingly, Themis T-cell conditional knockout mice died from severe CD8+-dependent lung immunopathology in chronic viral infection, showing Themis importance in establishing T cell exhaustion. We found that Themis-deficient CD8+ T cells were hyperactivated at the single-cell level - producing more TNF and IFN{gamma} compared to wild-type counterparts - but defective in population-level expansion. Moreover, TCF-1 and TOX expression were inhibited in Themis-deficient CD8+ T cells, thereby impairing differentiation of exhausted T cell precursors (T-pex) and maintenance of terminally exhausted T cells (T-ex), respectively. Mechanistically, Themis initially promotes TCR signaling to induce PD-1 expression and subsequently mediates PD-1 signaling. In the latter, Themis binds to PD-1 and promotes PD-1 phosphorylation and its recruitment of SHP2, thereby acting as a negative regulator to inhibit T cell effector functions. Without Themis, the orderly regulation of TCR and PD-1 signaling, and therefore exhaustion, is disrupted. Thus, our results unequivocally demonstrate that Themis-mediated early TCR signaling plays a decisive role in T cell exhaustion and provide a novel mechanism of PD-1 signaling through Themis.

immunology↗

LUMI-lab: a Foundation Model-Driven Autonomous Platform Enabling Discovery of New Ionizable Lipid Designs for mRNA Delivery

The complexity of molecular discovery requires autonomous systems that efficiently explore vast and uncharted chemical spaces. While integrating artificial intelligence (AI) with robotic automation has accelerated discovery, its application remains constrained in fields with scarce historical data. One such challenge is the design of lipid nanoparticles (LNPs) for mRNA delivery, which has relied on expert-driven design and is hindered by limited datasets. Here, we introduce LUMI-lab, a self-driving lab (SDL) system that enables efficient learning with minimal wet-lab data by integrating a molecular foundation model with an automated active-learning experimental workflow. Through ten iterative cycles, LUMI-lab synthesized and evaluated over 1,700 LNPs, identifying ionizable lipids with superior mRNA transfection potency in human bronchial cells compared to clinically approved benchmarks. Unexpectedly, it autonomously uncovered brominated lipid tails as a novel feature enhancing mRNA delivery. In vivo validation further confirmed that inhalation of LNPs containing the top-performing lipid, LUMI-6, achieved 20.3% gene editing efficacy in lung epithelial cells in murine models, surpassing the highest efficiency reported for inhaled LNP-mediated CRISPR-Cas9 delivery in mice to our knowledge. These findings demonstrate LUMI-lab as a powerful, data-efficient platform for advancing mRNA delivery, highlighting the potential of AI-driven autonomous systems to accelerate innovation in material science and therapeutic discovery.

biochemistry↗

gcSV: a unified framework for comprehensive structural variant detection

The characterization of structural variants (SVs) is fundamental to genomic studies and advanced computational approaches are on demand to exert the ability of the ubiquitous high-throughput sequencing data. Herein, we propose gcSV, a read-length agnostic alignment-based approach to well-handle the issues of genome repeats, SV breakpoints and read alignments/assemblies for comprehensive, cost-effective and versatile SV calling. For long reads, its yield is 20-38% higher than state-of-the-art tools in HG002 benchmark. For hybrid sequencing, it provides a cost-effective solution (2-4x long plus 30-60x short reads) to achieve even higher yield than that of state-of-the-art tools using 30x long reads. For short reads, gcSV also achieves over 8% higher precision without any loss of sensitivity. Furthermore, gcSV confidently brings over 93,000 novel SVs comparing to the official callset of 1000 Genomes Project Phase4. The results suggest that gcSV is promising to make valuable SV discoveries in many cutting-edge studies.

bioinformatics↗

Lactobacillus acidophilus Attenuates Polyethylene Glycol-Induced Susceptibility to Citrobacter rodentium Infection via Microbiota Modulation

ObjectivePolyethylene glycol (PEG), a globally prevalent laxative, is extensively utilized for bowel preparation prior to colonoscopy or abdominal surgery owing to its exceptional safety profile. Nevertheless, emerging evidence suggests that PEG administration may induce significant alterations in colonic microbiota composition, with dysbiotic effects persisting for over two weeks. The potential implications of such microbiota perturbations on the colonization and invasion of opportunistic pathogens remain underexplored. Methods and AnalysisTo investigate this, we employed a murine model infected with Citrobacter rodentium (C.R.), a surrogate for Enteropathogenic Escherichia coli (EPEC) and Enterohemorrhagic Escherichia coli (EHEC), following PEG-induced bowel preparation. ResultsThe severity of infectious enteritis was assessed, and the prophylactic efficacy of Lactobacillus acidophilus (LAC) supplementation was evaluated. Our findings indicate that PEG administration significantly elevated C.R. load, enhanced virulence gene expression, and exacerbated intestinal inflammation post-infection, with the infection window extending approximately 14 days. Through fecal metagenomic analysis and co-housing experiments, we demonstrated that PEG-associated enteritis is critically mediated by gut microbiota dysbiosis. Furthermore, supplementation with LAC was shown to mitigate susceptibility to C.R. infection. ConclusionsThese results suggest that PEG increases intestinal susceptibility to infection in a microbiota-dependent manner, highlighting the therapeutic potential of LAC in restoring microbial homeostasis.

microbiology↗

CDP-DAG synthases regulate plant growth and broad-spectrum disease resistance

Phosphatidic acid (PA) functions as a cell membrane component and signaling molecule in plants. PA metabolism has multiple routes, in one of which PA is converted into cytidine diphosphate diacylglycerol (CDP-DAG) by CDP-DAG synthases (CDSs). CDS genes are highly conserved in plants. Here, we found that knock-down of the CDS gene enhanced the resistance of Arabidopsis thaliana to multiple pathogens, with a growth penalty. When Arabidopsis leaves were treated with chitin or flg22, reactive oxygen species (ROS) production in cds mutants was significantly higher than that in the wild-type (WT). Similarly, phosphorylation of mitogen-activated protein kinases (MAPKs) in the cds1cds2 double mutant was significantly increased compared to the WT. By integrating lipidomics, transcriptomics, and metabolomics data, PA accumulation was observed in mutants cds1cds2, activating the jasmonic acid (JA) and salicylic acid (SA) signaling pathway, and increasing transcript levels of plant defense-related genes. Significant accumulation of the downstream metabolites including serotonin and 5-methoxyindole was also found, which plays important roles in plant immunity. In conclusion, our study indicated the role of CDSs in broad-spectrum disease resistance in Arabidopsis and that CDSs are involved in plant metabolic regulation.

plant biology↗

Simultaneous, real-time tracking of many neuromodulatory signals with Multiplexed Optical Recording of Sensors on a micro-Endoscope

Dozens of extracellular molecules jointly impact a given neuron, yet we lack methods to simultaneously record many such signals in real time. We developed a probe to track ten or more neuropeptides and neuromodulators using spatial multiplexing of genetically encoded fluorescent sensors. Cultured cells expressing one sensor at a time are immobilized at the front of a gradient refractive index (GRIN) lens for 3D two-photon imaging in vitro and in vivo. The sensor identity and detection sensitivity of each cell are determined via robotic dipping of the probe into wells containing various ligands and concentrations. Using this probe, we detected stimulation-evoked release of multiple neuromodulators in acute brain slices. We also tracked endogenous and drug-evoked changes in cerebrospinal fluid composition in the awake mouse lateral ventricle, which triggered downstream activation of the choroid plexus epithelium. Our approach offers a first step towards quantitative, real-time, high-dimensional tracking of brain fluid composition.

neuroscience↗

A Diverse Genetic Basis for Metabolic Reactions is Revealed Through Pangenome analysis

Sequenced genomes for thousands of strains of a bacterial species allow for a comprehensive analysis of its pangenome. We present a pangenome study of Escherichia colis metabolism by formulating gene-to-protein-to-reaction associations (GPRs) for about 2,700 metabolic reactions in 2,377 fully sequenced strains. On one hand, these GPRs reconstruct strain-specific networks that allow computational predictions (and experimental validation) of metabolic phenotypes, while on the other hand, they give the genetic basis for a given metabolic reaction in every strain. A pangenome-wide analysis of GPRs shows that: 1) We can reveal the genetic basis for a specific metabolic property at the species level; 2) The genetic basis for many metabolic reactions is diverse; 3) Many rare genes show variation in the genes genomic neighborhood which often contain genes from transposable elements, 4) Many rare genes show large-scale fragmentation and horizontal gene transfer (>11,000 rare genes in 2,377 strains); and 5) The aromatic amino acids and branched chain amino acids pathways are enriched with rare genes, with Acetolactate synthase having 29 distinct genes. Thus, analysis of GPRs across the pangenome reveals a complex dynamic evolutionary history of metabolism, revealing the role of conserved, fragmented, and horizontally transferred metabolic genes.

systems biology↗

ST-FFPE-mIF: Integrating Spatial Transcriptomics and Multiplex Immunofluorescence in Formalin-Fixed Paraffin-Embedded Tissues Using Stereo-seq

Stereo-seq is the state-of-the-art technique, which allows capturing of spatial transcriptomic data at sub-cellular resolution and in large scale of view. Stereo-seq FFPE technique is recently launched with the capability to obtain spatially resolved gene expression in FFPE tissue sections. However, the omic information is limited to transcriptome. To delineate spatial molecular hierarchy from transcriptome to phenome, we present the protocol that implements nine-plex immunofluorescence staining with detection of spatial transcriptomics in one FFPE tissue section (short for ST-FFPE-mIF). This protocol details the modified biochemistry procedure and also provides analytical framework to achieve single-cell resolution through nuclear or membrane staining-based cell segmentation. We demonstrated the application of ST-FFPE-mIF in colorectal cancer sample to illustrate how ST-FFPE-mIF facilitates a robust analysis of spatially resolved multi-omic data at the single-cell level.

biochemistry↗

A pan-cancer atlas of T cell targets

T-cell-based immunotherapies have revolutionized cancer treatment, yet only a minority of patients are eligible for these approaches, significantly constrained by the limited knowledge of tumor-specific antigens. Here we present ImmunoVerse, a comprehensive map of T cell targets across 21 cancer types, revealing actionable tumor-specific targets in 89% of tumors analyzed. To define the repertoire of actionable T cell targets, we conducted an exhaustive pan-cancer analysis, integrating data from 7,188 RNA-Seq, 1,771 immunopeptidomes from 512 biological samples and 208 single-cell cancer datasets using novel AI methods, and compared these against 17,384 normal samples covering 51 tissues. Our analysis uncovered 62 viable surface protein targets and 28,446 tumor-specific HLA-presented antigens, deriving from 11 distinct molecular events, across 21 tumor types. Among these, we identified 5,928 previously uncharacterized neoantigens, new tumor self-antigens, peptides derived from tumor-specific cryptic ORFs, tumor-associated microbial targets and a novel splicing-derived PMEL peptide (sPMEL) with enhanced abundance and safety compared to the canonical clinical targets. We successfully expanded sPMEL-specific T cells, validating the therapeutic potential of these targets in functional assays. We highlight 153 promising new tumor targets and experimentally validate 19 targets representing six antigen classes. In addition to being the most comprehensive atlas of targets in scope, ImmunoVerse offers the most extensively annotated resource with key parameters for target selection, providing critical insights for therapeutic prioritization and clinical translation. To catalyze therapeutic development, we released our pan-cancer target atlas through an interactive web portal (https://www.immuno-verse.com) and made the accompanying toolkits available to the scientific community. This work redefines the landscape of therapeutic T cell targets and provides a foundational resource to unlock immunotherapy development across multiple cancers previously considered intractable.

cancer biology↗

Sequencing-based Spatial Transcriptomics with scRNA-seq Sensitivity

The advent of spatial transcriptomics has dramatically expanded our ability to study the vast network of cell-cell interactions at the molecular level in tissue. Among current methods, sequencing-based approaches have great potential in discovering because of its unbiased capture. In the last couple of years, the spatial resolution for the capture addresses has been significantly improved from 100 m to <1 m, well below the size of a mammalian cell. However, the capture efficiency has always been a pain point, [~]one order of magnitude lower than that of single cell RNA sequencing (scRNA-seq). The low capture efficiency limits the depth and breadth of its applications in the study of complex biological systems and diseases. Here, we introduce Salus Spatial transcriptomic system (Salus-STS), which provides [~]1 m capture resolution and a capture efficiency [~]1 order of magnitude higher than other current methods. Analysis with sub-cellular resolution becomes practical for sequencing-based spatial transcriptomics.

molecular biology↗

Development of conditional-siRNA programmable riboswitch for targeting adverse cardiac remodeling

Heart Failure (HF) remains a global epidemic and a significant healthcare burden, with an unmet need for novel therapies to target the preceding pathological hypertrophy in vulnerable patients. Here we report the development of novel conditional-siRNA (Cond- siRNA) constructs that are selectively activated by disease-specific RNA biomarkers to enable cell-specific inhibition of a target disease-causing RNA. We designed a Cond- siRNA that can be activated by nppa mRNA, upregulated specifically in CMs under pathological stress, to silence the key pro-hypertrophic gene calcineurin by the effector siRNA. In cellular models including neonatal rat ventricular myocyte (NRVM) and rat cardiomyocyte cell-line (H9C2), Cond-siRNA exhibited low baseline activity in the absence of the disease biomarker but achieved targeted calcineurin silencing upon nppa mRNA induction by phenylephrine (PE)-induced stress in a two-dimensional (2D) cell culture system and pressure overload in three-dimensional (3D) heart-on a chip system. NRVM transfection with the Cond-siRNA resulted in a decreased expression of calcineurin mRNA specifically after PE or pressure-overload treatment, but not after vehicle treatment, proving nppa mRNA-specific activation of the effector siRNA against calcineurin. Specificity was confirmed as Cond-siRNA did not significantly silence calcineurin in cardiac fibroblasts and T cells, lacking nppa expression. Reduced calcineurin protein levels and NFATc1 nuclear translocation correlated with decreased NRVM hypertrophy after PE treatment, confirming Cond-siRNAs efficacy. This study offers proof-of-concept for Cond-siRNA as a targeted therapy to mitigate hypertrophic progression, paving the way for novel HF treatments. One sentence summaryConditional-siRNA targeting adverse cardiac remodeling GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/633434v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1b6532borg.highwire.dtl.DTLVardef@10e3836org.highwire.dtl.DTLVardef@8c839eorg.highwire.dtl.DTLVardef@1152883_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

MicroRNA signatures of VO2peak in older adult participants of the Study of Muscle, Mobility and Aging

BackgroundPeak oxygen consumption during exercise (VO2peak), is a direct measure of cardiorespiratory fitness (CF), a key indicator of physical function and overall health. However, the molecular changes that underpin VO2peak variation are not clear. Our objective is to understand the miRNA signatures that relate to VO2peak variation, which could provide insights to novel mechanisms that contribute to low VO2peak. MethodsWe used small RNA sequencing to analyze serum samples from 72 participants (70-79 yrs old, 53% female) of the Study of Muscle, Mobility and Aging (SOMMA). We analyzed samples from individuals with low or high VO2peak (N=18/group) as well as samples from 36 randomly selected participants spanning the entire spectrum of VO2peak. We used LIMMA analysis package for regression analysis and to identify differentially expressed miRNAs. We used receiver operating characteristic curve analysis to evaluate the Area Under the Curve (AUC) and sensitivity and specificity rates. ResultsWe identified 1,055 miRNAs expressed in all serum samples. Expression of 65 miRNAs differed between participants with low and high VO2peak (p < 0.05). After p-value adjustment, expression of 5 miRNAs (miR-1301-3p, -431-5p, -501-5p, -519a-3p, and -18a-3p) remained significantly different (FDR = 0.05). The five miRNAs had AUC ranging from 0.77 to 0.84. The optimal sensitivity and specificity ranged from 70 to 80% and 80 to 90%, respectively. After adjustment for age and sex covariates, 46 miRNAs significantly correlated with VO2peak (p < 0.05) and miR-519a-3p remained significant based on adjusted of p-values. ConclusionsWe identified a miRNA signature of VO2peak in older individuals that might provide insights to novel mechanisms that drive low VO2peak. Future studies will validate the findings in a larger, longitudinal study cohort.

molecular biology↗

Accumbal acetylcholine signals associative salience

Learning is driven by prediction errors, which determine what is learned, and salience, which controls the learning rate. Dopamine in the nucleus accumbens correlates with prediction errors, but salience mechanisms are less clear. We hypothesized that acetylcholine acts as a salience signal, as it regulates dopamine-induced plasticity. To test this, we recorded acetylcholine and dopamine dynamics in rats across three learning tasks. Our findings reveal a characteristic pattern of evolving neuromodulator responses during learning. First, indiscriminate cholinergic dips appeared, then dopamine responses differentiated based on predicted value, followed by the cholinergic dips also varying by value. Stable performance required this full pattern, and acetylcholine dips could be decoupled from value by changing reward contingencies. The observed acetylcholine dynamics fit an associative salience term predicted by hybrid attentional associative learning models, suggesting that dopamine and acetylcholine act complementarily to determine the content and rate of learning. TeaserAcetylcholine shapes learning rate by signaling the salience of predictive cues.

neuroscience↗

Role of RSPO3 in Estrogen-mediated Sex Differences in Body Fat Distribution: A Single-cell Data-driven Study

Obesity is a global health concern affecting more than one-third of the adult population worldwide. Epidemiological studies indicate that body fat distribution, more than overall adiposity, is a key risk factor for obesity-related diseases. Genome-wide association studies revealed that RSPO3 is associated with body fat distribution. Additionally, marked sex differences in body fat distribution are largely influenced by estrogen, suggesting that exploring the relationship between estrogen and RSPO3 expression may illuminate the mechanisms underlying the sexual dimorphism of fat distribution. We revisited a comprehensive set of gene expression data from humans and mice to explore these mechanisms. We assessed RSPO3 expression in male and female adipose tissues and utilized single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics to examine RSPO3s function within different tissues. Our findings confirmed significantly higher RSPO3 expression in male adipose tissue compared to female. Furthermore, our data for the first time suggest that estrogen plays a crucial role in fat distribution, as blocking estrogen signaling upregulates RSPO3 expression. In mouse liver, we observed a correlation between sex-specific ADK overexpression and RSPO3 expression, resulting in increased obesity and hepatocyte expansion via WNT/{beta}-catenin signaling in male mice. This study sheds light on how estrogen influences sexual dimorphism in fat distribution and underscores RSPO3s vital role in this process. These insights open new avenues for targeted therapeutic interventions addressing obesity and metabolic diseases with a focus on sex-specific factors.

bioinformatics↗

Bovine Formative Embryonic Stem Cell Plasticity in Embryonic and Extraembryonic Differentiation

Bovine embryonic stem cells (bESCs) can greatly enhance understanding of bovine embryonic development and applications for disease-resistance, biomedical and zoonotic pre-clinical models. However, formative bESCs with distinct morphology and complete differentiation capacity are still unreported. We document here the generation of bESCs which are pluripotent both in vitro and in vivo, and efficiently converted into neural progenitor cells (NPCs) and primordial germ cell-like cells (PGCLCs) by direct differentiation. These cells exhibited distinct metabolic features from human and mouse ESCs and early embryos. Formative bESCs contributed to a wide range of cell types within embryonic and extraembryonic tissues after aggregating with mouse and bovine embryos. The establishment of bovine formative ESCs with dual developmental plasticity represents a milestone for agricultural biotechnology and decoding the underlying mechanism of bona fide bovine pluripotency. Summary statementGenerating bovine ESCs would greatly enhance understanding of bovine embryonic development and bioengineering of cattle for disease-resistance, biomedical and zoonotic pre-clinical models.

developmental biology↗

Red-shifted GRAB acetylcholine sensors for multiplex imaging in vivo

The neurotransmitter acetylcholine (ACh) is essential in both the central and peripheral nervous systems. Recent studies highlight the significance of interactions between ACh and various neuromodulators in regulating complex behaviors. The ability to simultaneously image ACh and other neuromodulators can provide valuable information regarding the mechanisms underlying these behaviors. Here, we developed a series of red fluorescent G protein-coupled receptor activation-based (GRAB) ACh sensors, with a wide detection range and expanded spectral profile. The high-affinity sensor, rACh1h, reliably detects ACh release in various brain regions, including the nucleus accumbens, amygdala, hippocampus, and cortex. Moreover, rACh1h can be co-expressed with green fluorescent sensors in order to record ACh release together with other neurochemicals in various behavioral contexts using fiber photometry and two-photon imaging, with high spatiotemporal resolution. These new ACh sensors can therefore provide valuable new insights regarding the functional role of the cholinergic system under both physiological and pathological conditions.

neuroscience↗

In vivo multiplex imaging of dynamic neurochemical networks with designed far-red dopamine sensors

Neurochemical signals like dopamine (DA) play a crucial role in a variety of brain functions through intricate interactions with other neuromodulators and intracellular signaling pathways. However, studying these complex networks has been hindered by the challenge of detecting multiple neurochemicals in vivo simultaneously. To overcome this limitation, we developed a single-protein chemigenetic DA sensor, HaloDA1.0, which combines a cpHaloTag-chemical dye approach with the G protein-coupled receptor activation-based (GRAB) strategy, providing high sensitivity for DA, sub-second response kinetics, and an extensive spectral range from far-red to near-infrared. When used together with existing green and red fluorescent neuromodulator sensors, Ca2+ indicators, cAMP sensors, and optogenetic tools, HaloDA1.0 provides high versatility for multiplex imaging in cultured neurons, brain slices, and behaving animals, facilitating in-depth studies of dynamic neurochemical networks.

neuroscience↗

Phosphotyrosine Signal Profiling of Clinical CAR-T Reveals Tonic Signaling Associated with Therapeutic Efficacy

Chimeric Antigen Receptor T (CAR-T) therapies have revolutionized the treatment of cancers such as relapsed and refractory B cell malignancies. However, the precise therapeutic mechanism of CAR-T action remain to be elucidated. In this study, we systematically analyzed CAR signaling via phosphotyrosine (pTyr) proteomics in CAR-T cells from both clinical patients and healthy donors. We found that CAR-T products from clinical patients displayed heightened tyrosine phosphorylation, particularly in the JAK-STAT, MAPK and TCR signaling cascades. We also identified the significantly regulated pTyr sites in primary CAR-T cells under tonic signaling or upon stimulation by antigen-presenting CD19-K562 cells. Although both CD28{zeta} and 4-1BB{zeta} CAR-T cells exhibited comparable pTyr changes, CD28{zeta} CAR-T cells displayed a more pronounced activation in the TCR signaling pathway. Additionally, comparative analysis between clinical and primary CAR-T cells suggested that CAR-T products were subject to heightened tonic signaling, which may be related to therapeutic relapse. Our findings reveal the state of clinical CAR-T products and refine the CAR-T signal transduction network, providing comprehensive insights and informed guidance for CAR-T therapies.

immunology↗